Hvy-bolter lost on mission start

My heavy weapon crusader has a plasma cannon on configuration 1, and heavy flammer on configuration 2. Every time I start a mission equiping a hvy-bolter on the plasma-cannon slot the mission keeps starting with the plasma and I lose the hvy-bolter.

Weird thing is that this doesnt happend if i place it on slot 2 instead of the hvy-flammer.

Yeah this is a known bug that is being worked on. What you can try though is do not equip anything in that slot when you lose the item and then completely exit the game and restart. Usually fixes the problem for me.